From fec95dfbf0abe4175649e399eb1fcd698d482a9a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 30 Mar 2017 17:54:16 +0200 Subject: Add checkcontrols, updates, see ChangeLog --- man/IM1xIPC81.Rd | 2 +- man/IM1xVibrio.Rd | 8 ++++---- man/XY.Rd | 2 +- man/antifoul.Rd | 12 ++++++------ man/checkcontrols.Rd | 12 ++++++------ man/checkexperiment.Rd | 4 ++-- man/checksubstance.Rd | 14 +++++++------- man/drcfit.Rd | 20 ++++++++++---------- man/drdata.Rd | 22 +++++++++++----------- man/drfit-package.Rd | 2 +- man/drfit.Rd | 22 +++++++++++----------- man/drplot.Rd | 26 +++++++++++++------------- man/linlogitf.Rd | 6 +++--- 13 files changed, 76 insertions(+), 76 deletions(-) mode change 100755 => 100644 man/linlogitf.Rd (limited to 'man') diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd index dda0c3b..5994f6a 100644 --- a/man/IM1xIPC81.Rd +++ b/man/IM1xIPC81.Rd @@ -29,7 +29,7 @@ print(rIM1xIPC81.drc,digits=4) } \source{ - Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, + Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1 cell diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd index cb0bd48..d3258fb 100644 --- a/man/IM1xVibrio.Rd +++ b/man/IM1xVibrio.Rd @@ -6,9 +6,9 @@ This is the raw data documenting the influence of the alkyl chain length in 3 position on the toxicity to the marine luminescent bacteria \emph{V. fischeri}. The substances are named according to the UFT naming scheme of - these substances. - IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate, - IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and + these substances. + IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate, + IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate. } \usage{data(IM1xVibrio)} @@ -28,7 +28,7 @@ print(rIM1xVibrio.drc, digits = 4) } \source{ - Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, + Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1 cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404 diff --git a/man/XY.Rd b/man/XY.Rd index 8022264..82a48fe 100644 --- a/man/XY.Rd +++ b/man/XY.Rd @@ -3,7 +3,7 @@ \alias{XY} \title{Dose-Response data for two substances X and Y} \description{ - This is just a sample Lemna growth rate data set for two substances + This is just a sample Lemna growth rate data set for two substances arbitrarily named X and Y. } \usage{data(XY)} diff --git a/man/antifoul.Rd b/man/antifoul.Rd index 21ae885..e782636 100644 --- a/man/antifoul.Rd +++ b/man/antifoul.Rd @@ -3,9 +3,9 @@ \alias{antifoul} \title{Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells} \description{ - This data set shows the response of the rat leukaemic cell line IPC-81 to + This data set shows the response of the rat leukaemic cell line IPC-81 to dilution series of tributyltin chloride (TBT) and Zink Pyrithione as retrieved - from the "cytotox" database of the UFT Department of Bioorganic Chemistry on + from the "cytotox" database of the UFT Department of Bioorganic Chemistry on February 25, 2004 } \usage{data(antifoul)} @@ -15,15 +15,15 @@ database are also present. } \examples{ -rantifoul.ED50 <- drfit(antifoul, +rantifoul.ED50 <- drfit(antifoul, linlogit = TRUE, logit = TRUE, weibull = TRUE, - chooseone = FALSE, + chooseone = FALSE, showED50 = TRUE, EDx = c(10)) print(rantifoul.ED50, digits = 5) -rantifoul.drc <- drcfit(antifoul, +rantifoul.drc <- drcfit(antifoul, linlogit = TRUE, logit = TRUE, weibull = TRUE, - chooseone = FALSE, + chooseone = FALSE, showED50 = TRUE, EDx = c(10)) print(rantifoul.drc, digits = 5) } diff --git a/man/checkcontrols.Rd b/man/checkcontrols.Rd index b155643..3941a69 100644 --- a/man/checkcontrols.Rd +++ b/man/checkcontrols.Rd @@ -6,7 +6,7 @@ experiments from a specified database. } \usage{ - checkcontrols(last = 10, id = NULL, db = "cytotox", organism = "Vibrio fischeri", + checkcontrols(last = 10, id = NULL, db = "cytotox", organism = "Vibrio fischeri", endpoint = "\%", qcc = c("R", "xbar")) } \arguments{ @@ -29,9 +29,9 @@ The endpoint that should be used for selecting the data. Only important if the database "ecotox" is used. Defaults to "\%".} \item{qcc}{ - The type of quality control charts to be plotted. By default, an R chart - (showing ranges of control values within plates/experiments), and an - xbar chart (showing means) are generated. + The type of quality control charts to be plotted. By default, an R chart + (showing ranges of control values within plates/experiments), and an + xbar chart (showing means) are generated. } } \value{ @@ -41,8 +41,8 @@ \dontrun{checkcontrols(15)} } \author{ - Johannes Ranke - \email{jranke@uni-bremen.de} + Johannes Ranke + \email{jranke@uni-bremen.de} \url{http://www.uft.uni-bremen.de/chemie/ranke} } \keyword{database} diff --git a/man/checkexperiment.Rd b/man/checkexperiment.Rd index 0edf2fb..6a682fa 100644 --- a/man/checkexperiment.Rd +++ b/man/checkexperiment.Rd @@ -29,8 +29,8 @@ \dontrun{checkplate(3)} } \author{ - Johannes Ranke - \email{jranke@uni-bremen.de} + Johannes Ranke + \email{jranke@uni-bremen.de} \url{http://www.uft.uni-bremen.de/chemie/ranke} } \keyword{database} diff --git a/man/checksubstance.Rd b/man/checksubstance.Rd index 387785f..6182fce 100644 --- a/man/checksubstance.Rd +++ b/man/checksubstance.Rd @@ -6,8 +6,8 @@ the data. } \usage{ - checksubstance(substance, db = "cytotox", experimentator = "\%", - celltype = "\%", enzymetype = "\%", organism = "\%", + checksubstance(substance, db = "cytotox", experimentator = "\%", + celltype = "\%", enzymetype = "\%", organism = "\%", endpoint = "\%", whereClause = "1", ok = "\%") } @@ -17,7 +17,7 @@ \item{db}{ The database to be used. Currently, the databases "cytotox" and "enzymes" of the UFT Department of Bioorganic Chemistry are supported (default is - "cytotox").} + "cytotox").} \item{experimentator}{ The name of the experimentator whose data is to be used. Default is "\%", which means that data from all experimentators are shown.} @@ -35,10 +35,10 @@ The endpoint that should be used for selecting the data. Only important if the database "ecotox" is used. Defaults to "\%".} \item{whereClause}{ - With this argument, additional conditions for the SQL query can be set, + With this argument, additional conditions for the SQL query can be set, e.g. "plate != 710". The default is 1 (in SQL syntax this means TRUE).} \item{ok}{ - With the default value "\%", all data in the database is retrieved for the + With the default value "\%", all data in the database is retrieved for the specified substance.} } \value{ @@ -49,8 +49,8 @@ \dontrun{checksubstance("IM14 BF4")} } \author{ - Johannes Ranke - \email{jranke@uni-bremen.de} + Johannes Ranke + \email{jranke@uni-bremen.de} \url{http://www.uft.uni-bremen.de/chemie/ranke} } \keyword{database} diff --git a/man/drcfit.Rd b/man/drcfit.Rd index b10418a..67462ba 100644 --- a/man/drcfit.Rd +++ b/man/drcfit.Rd @@ -7,7 +7,7 @@ } \usage{ drcfit(data, chooseone = TRUE, probit = TRUE, logit = FALSE, - weibull = FALSE, linlogit = FALSE, level = 0.95, + weibull = FALSE, linlogit = FALSE, level = 0.95, showED50 = FALSE, EDx = NULL) } \arguments{ @@ -67,7 +67,7 @@ \value{ A dataframe with the attribute \code{models} holding a list of the fitted dose-response models of class \code{\link{nls}}. The dataframe has at least - one line for each substance. + one line for each substance. The following variables are in the dataframe: \item{Substance}{ @@ -89,14 +89,14 @@ If the data did not show a mean response < 0.5 at the highest dose level, the modeltype is set to \dQuote{inactive}. If the mean response at the lowest dose is smaller than 0.5, the modeltype is set to \dQuote{active}. - In both cases, no fitting procedure is carried out. If the fitted ED50 + In both cases, no fitting procedure is carried out. If the fitted ED50 is higher than the highest dose, \dQuote{no fit} is given here. } \item{logED50}{ The decadic logarithm of the ED50 } \item{low \%}{ - The lower bound of the confidence interval of log ED50. + The lower bound of the confidence interval of log ED50. The name of the column depends on the requested confidence \code{level}. } \item{high \%}{ @@ -112,16 +112,16 @@ } \item{a}{ For the linlogit model, this is the parameter e from \code{\link{BC.4}}. - For the probit and the logit model, this is the ED50. For the weibull - model, this is parameter e from \code{\link{W1.2}}. Note that the Weibull + For the probit and the logit model, this is the ED50. For the weibull + model, this is parameter e from \code{\link{W1.2}}. Note that the Weibull model is fitted to the untransformed data. } \item{b}{ For the linlogit, probit, logit and weibull models, these are the - parameters b from \code{\link{BC.4}}, \code{\link{LN.2}}, + parameters b from \code{\link{BC.4}}, \code{\link{LN.2}}, \code{\link{LL.2}} and \code{\link{W1.2}}, respectively. Note that the parameter definitions (and in the case of Weibull, the model - used) are different to the ones used in \code{\link{drfit}}. + used) are different to the ones used in \code{\link{drfit}}. } \item{c}{ Only the \dQuote{linlogit} fit produces a third parameter \code{c}, which is @@ -140,14 +140,14 @@ r <- drcfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20)) format(r, digits = 2) } \note{There is a demo for each dataset that can be accessed by - \code{demo(dataset)}} + \code{demo(dataset)}} \seealso{ Further examples are given in help pages to the datasets \code{\link{antifoul}}, \code{\link{IM1xIPC81}} and \code{\link{IM1xVibrio}}. } \author{ - Johannes Ranke \email{jranke@uni-bremen.de} + Johannes Ranke \email{jranke@uni-bremen.de} \url{http://www.uft.uni-bremen.de/chemie/ranke} The functionality of the drc package used under the hood in this function was written by Christian Ritz. diff --git a/man/drdata.Rd b/man/drdata.Rd index 8f545da..4fb6740 100644 --- a/man/drdata.Rd +++ b/man/drdata.Rd @@ -2,11 +2,11 @@ \alias{drdata} \title{Get dose-response data via RODBC} \description{ - Get dose-response data from an adequate ODBC data source + Get dose-response data from an adequate ODBC data source } \usage{ - drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81", - enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence", + drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81", + enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence", whereClause = "1", ok = "'ok','no fit'") } \arguments{ @@ -18,11 +18,11 @@ which means that data from all experimentators are retrieved.} \item{db}{ The database to be used. Currently, the databases "cytotox", "enzymes" - and "ecotox" of the UFT Department of Bioorganic Chemistry are - supported (default is "cytotox").} + and "ecotox" of the UFT Department of Bioorganic Chemistry are + supported (default is "cytotox").} \item{celltype}{ Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are - supported.} + supported.} \item{enzymetype}{ Currently, only data for AChE, GR and GST are supported.} \item{organism}{ @@ -32,9 +32,9 @@ The endpoint that should be used for selecting the data. Only important if the database "ecotox" is used. Defaults to "Luminescence".} \item{whereClause}{ - With this argument, additional conditions for the SQL query can be set, + With this argument, additional conditions for the SQL query can be set, e.g. "plate != 710" (i.e. "Do not retrieve data for plate 710"). The - default is 1 (in SQL syntax this means TRUE).} + default is 1 (in SQL syntax this means TRUE).} \item{ok}{ With the default value "'ok','no fit'", only data that has been checked and set to "ok" or "no fit" in the database is retrieved. The argument "no fit" @@ -58,7 +58,7 @@ myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the respective data source with data source name (DSN) "cytotox". For my setting using unixodbc, I am using the file \file{/etc/odbcinst.ini} - containing: + containing: \tabular{lll}{ [MySQL] \tab \tab \cr Description \tab = \tab MySQL driver for ODBC \cr @@ -83,8 +83,8 @@ \dontrun{drdata(c("TBT","ZnPT2"))} } \author{ - Johannes Ranke - \email{jranke@uni-bremen.de} + Johannes Ranke + \email{jranke@uni-bremen.de} \url{http://www.uft.uni-bremen.de/chemie/ranke} } \keyword{IO} diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd index 696cee9..06a147f 100644 --- a/man/drfit-package.Rd +++ b/man/drfit-package.Rd @@ -16,7 +16,7 @@ of R for chemists. Author and Maintainer: Johannes Ranke } \note{There is a demo for each dataset that can be accessed by - \code{demo(dataset)}} + \code{demo(dataset)}} \keyword{ package } \keyword{ models } \keyword{ regression } diff --git a/man/drfit.Rd b/man/drfit.Rd index 3729550..ec7fa70 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -9,7 +9,7 @@ drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE, weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA, allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, b0 = 2, f0 = 0, - showED50 = FALSE, + showED50 = FALSE, EDx = NULL, EDx.tolerance = 1e-4) } \arguments{ @@ -32,11 +32,11 @@ \item{probit}{ A boolean defining if cumulative density curves of normal distributions \code{\link{pnorm}} are fitted against the decadic logarithm of the dose. - Default ist TRUE.} + Default ist TRUE.} \item{logit}{ A boolean defining if cumulative density curves of logistic distributions \code{\link{plogis}} are fitted to the decadic logarithm of the dose. - Default is FALSE.} + Default is FALSE.} \item{weibull}{ A boolean defining if the cumulative density curves of weibull distributions (\code{\link{pweibull}} with additionall location parameter and scale=1) @@ -87,14 +87,14 @@ \value{ A dataframe with the attribute \code{models} holding a list of the fitted dose-response models of class \code{\link{nls}}. The dataframe has at least - one line for each substance. + one line for each substance. For the \dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the parameter \code{a} that is reported coincides with the logED50, i.e the logED50 is one of the model parameters that is being fitted. Therefore, a confidence interval for the confidence level \code{level} is calculated using the \code{\link[MASS:confint]{confint.nls}} function and listed. - + The following variables are in the dataframe: \item{Substance}{ The name of the substance @@ -115,14 +115,14 @@ If the data did not show a mean response < 0.5 at the highest dose level, the modeltype is set to \dQuote{inactive}. If the mean response at the lowest dose is smaller than 0.5, the modeltype is set to \dQuote{active}. - In both cases, no fitting procedure is carried out. If the fitted ED50 + In both cases, no fitting procedure is carried out. If the fitted ED50 is higher than the highest dose, \dQuote{no fit} is given here. } \item{logED50}{ The decadic logarithm of the ED50 } \item{low \%}{ - The lower bound of the confidence interval of log ED50. + The lower bound of the confidence interval of log ED50. The name of the column depends on the requested confidence \code{level}. } \item{high \%}{ @@ -139,7 +139,7 @@ \item{a}{ For the \dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the parameter \code{a} coincides with the logED50. In the case of the - \dQuote{weibull} model, \code{a} is a location parameter. + \dQuote{weibull} model, \code{a} is a location parameter. } \item{b}{ Parameter \code{b} in the case of the \dQuote{linlogit} fit is the variable @@ -165,7 +165,7 @@ r <- drfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20)) format(r, digits = 2) } \note{There is a demo for each dataset that can be accessed by - \code{demo(dataset)}} + \code{demo(dataset)}} \seealso{ Further examples are given in help pages to the datasets \code{\link{antifoul}}, \code{\link{IM1xIPC81}} and @@ -175,8 +175,8 @@ format(r, digits = 2) confidence intervals for EDx values via this package. } \author{ - Johannes Ranke - \email{jranke@uni-bremen.de} + Johannes Ranke + \email{jranke@uni-bremen.de} \url{http://www.uft.uni-bremen.de/chemie/ranke} } \keyword{models} diff --git a/man/drplot.Rd b/man/drplot.Rd index e9e4dd1..6b8a7bf 100644 --- a/man/drplot.Rd +++ b/man/drplot.Rd @@ -2,7 +2,7 @@ \alias{drplot} \title{Plot dose-response models} \description{ - Produce graphics of dose-response data and dose-response relationships + Produce graphics of dose-response data and dose-response relationships either combined or separately, for one or more substances. } \usage{ @@ -14,13 +14,13 @@ \item{drresults}{ A data frame as returned from \code{\link{drfit}}. } - \item{data}{ + \item{data}{ A data frame as returned from \code{\link{drdata}}. The data frame has to contain at least a factor called "substance", a vector called "unit" containing the unit used for the dose, a column "response" with the response values of the test system normalized between 0 and 1, a column "dose" with the numeric dose values and a factor called "dosefactor" - containing the dose as a factor. + containing the dose as a factor. } \item{dtype}{ A string describing if the raw data should be plotted ("raw"), or an error @@ -33,7 +33,7 @@ chosen. } \item{ctype}{ - This argument decides if horizontal lines are drawn to show the scatter of + This argument decides if horizontal lines are drawn to show the scatter of the control values (dose = 0), if there are more than three of them. Defaults to "none", further allowed values are "std" and "conf" for displaying the standard deviation of the controls or the confidence @@ -49,7 +49,7 @@ } \item{overlay}{ If TRUE, all output will be put into one graph, otherwise a separate graph - will be created for each substance. + will be created for each substance. } \item{xlim}{ The plot limits (min,max) on the dose axis. @@ -72,12 +72,12 @@ \code{\link{plot.default}} } \item{postscript}{ - If TRUE, (a) postscript graph(s) will be created. Otherwise, and if + If TRUE, (a) postscript graph(s) will be created. Otherwise, and if the pdf and png arguments are also FALSE, graphics will be displayed with a screen graphics device. } \item{pdf}{ - If TRUE, (a) pdf graph(s) will be created. Otherwise, and if + If TRUE, (a) pdf graph(s) will be created. Otherwise, and if the postscript, and png arguments are also FALSE, graphics will be displayed with a screen graphics device. } @@ -87,7 +87,7 @@ with a screen graphics device. } \item{bw}{ - A boolean deciding if the plots will be black and white or not. Default + A boolean deciding if the plots will be black and white or not. Default is TRUE. } \item{pointsize}{ @@ -107,7 +107,7 @@ \item{lpos}{ An optional argument defaulting to "topright" specifying the position of the legend by being passed to the legend function. See the help for the - legend function for all possiblities.} + legend function for all possiblities.} \item{devoff}{ If set to FALSE, the device will not be closed after creation of an overlay pdf, png or postscript graph, so texts and other elements can @@ -119,17 +119,17 @@ You will get plots of data and/or the fitted dose-response curves, on the screen and/or as postscript/pdf/png files, depending on the parameters. } -} +} \examples{ data(antifoul) r <- drfit(antifoul) \dontrun{drplot(r,antifoul)} } \note{There is a demo for each dataset that can be accessed by - \code{demo(dataset)}} + \code{demo(dataset)}} \author{ - Johannes Ranke - \email{jranke@uni-bremen.de} + Johannes Ranke + \email{jranke@uni-bremen.de} \url{http://www.uft.uni-bremen.de/chemie/ranke} } \keyword{models} diff --git a/man/linlogitf.Rd b/man/linlogitf.Rd old mode 100755 new mode 100644 index f091581..2c9ddc4 --- a/man/linlogitf.Rd +++ b/man/linlogitf.Rd @@ -22,13 +22,13 @@ } \value{ The response at dose x. -} +} \references{ van Ewijk, P. H. and Hoekstra, J. A. (1993) \emph{Ecotox Environ Safety} \bold{25} 25-32} \author{ - Johannes Ranke - \email{jranke@uni-bremen.de} + Johannes Ranke + \email{jranke@uni-bremen.de} \url{http://www.uft.uni-bremen.de/chemie/ranke} } \keyword{models} -- cgit v1.2.1